The DOI matches its Crossref record; 34 of the 36 references it cites were found in a registry or an index.
Global response of Saccharomyces cerevisiae to an alkylating agent
Open accessAbstract
DNA chip technology enables simultaneous examination of how ≈6,200 Saccharomyces cerevisiae gene transcript levels, representing the entire genome, respond to environmental change. By using chips bearing oligonucleotide arrays, we show that, after exposure to the alkylating agent methyl methanesulfonate, ≈325 gene transcript levels are increased and ≈76 are decreased. Of the 21 genes that already were known to be induced by a DNA-damaging agent, 18 can be scored as inducible in this data set, and surprisingly, most of the newly identified inducible genes are induced even more strongly than these 18. We examined 42 responsive and 8 nonresponsive ORFs by conventional Northern blotting, and 48 of these 50 ORFs responded as they did by DNA chip analysis, with magnitudes displaying a correlation coefficient of 0.79. Responsive genes fall into several expected and many unexpected categories. Evidence for the induction of a program to eliminate and replace alkylated proteins is presented.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Indeed, approximately 5% of the yeast genome is upregulated in response to various DNA-damaging agents (15, 23, 24).”
From A Role for Checkpoint Kinase-Dependent Rad26 Phosphorylation in Transcription-Coupled DNA Repair in Saccharomyces cerevisiae (2010) · cites this paper as [24]
Citations
Cites
Molecular cloning: A laboratory manual
Deininger, P. L. (1990) · Analytical Biochemistry · doi:10.1016/0003-2697(90)90595-z · Cited by 84,684
Friedberg, E. C., Walker, G. C., Siede, W., Wood, R. D., Schultz, R. A., & Ellenberger, T. (2005) · doi:10.1128/9781555816704 · Cited by 5,683
Expression monitoring by hybridization to high-density oligonucleotide arrays
Lockhart, D. J., Dong, H., Byrne, M. C., Follettie, M. T., Gallo, M. V., Chee, M. S., Mittmann, M., Wang, C., Kobayashi, M., Norton, H., et al. (1996) · Nature Biotechnology · doi:10.1038/nbt1296-1675 · Cited by 2,841
Bootsma, D., & Hoeijmakers, J. H. J. (1996) · Trends in Genetics · doi:10.1016/0168-9525(96)81408-9 · Cited by 2,285
A Genome-Wide Transcriptional Analysis of the Mitotic Cell Cycle
Cho, R. J., Campbell, M. J., Winzeler, E. A., Steinmetz, L. M., Conway, A. R., Wodicka, L. M., Wolfsberg, T. G., Gabrielian, A. E., Landsman, D., Lockhart, D. J., et al. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80114-8 · Cited by 2,024
A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae
Schmitt, M. E., Brown, T. A., & Trumpower, B. L. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.10.3091 · Cited by 1,344
SGD: Saccharomyces Genome Database
Cherry, J. M. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.1.73 · Cited by 1,145
Genome-wide expression monitoring in Saccharomyces cerevisiae
Wodicka, L. M., Dong, H., Mittmann, M., Ho, M.-H., & Lockhart, D. J. (1997) · Nature Biotechnology · doi:10.1038/nbt1297-1359 · Cited by 973
Characterization of the Yeast Transcriptome
Velculescu, V. E., Zhang, L., Zhou, W., Vogelstein, R. J., Basrai, M. A., Bassett, D. E., Hieter, P., Vogelstein, B., & Kinzler, K. W. (1997) · Cell · doi:10.1016/s0092-8674(00)81845-0 · Cited by 973
DNA damage-inducible transcripts in mammalian cells.
Fornace, A. J., Alamo, I., & Hollander, M. C. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.23.8800 · Cited by 624
Flagged first, then by citations
2 of the 36 references couldn’t be matched to a known paper.
Research works printed but not linked: 5
- P Herrlich, C Blattner, A Knebel, K Bender, H J Rahmsdorf Biol Chem 378, 1217–1229 (1997).
- 10.1128/mcb.13.7.4242-4250.1993 · DOI
- J B Bachant, S J Elledge DNA Repair in Prokaryotes and Lower Eukaryotes, DNA Damage and Repair, eds J A Nickoloff, M F Hoekstra (Humana, Totowa, NJ) 1 (1998).
- W Xiao, K K Singh, B Chen, L Samson Mol Cell Biol 13, 7213–7221 (1993).
- J E Landers, S L Cassel, D L George Cancer Res 57, 3562–3568 (1997).
Cited by
Sorted by citations
Items 401–420 of 420
Synthetic Regulation of Eukaryotic Gene Expression by Noncoding RNA
d’Espaux, L. (2013) · CaltechTHESIS (California Institute of Technology) · doi:10.7907/z9cr5rbp
Analyses of the MEC1 DNA Damage Pathway in Saccharomyces cerevisiae
Ainsworth, W. B. (2015) · doi:10.31390/gradschool_dissertations.1185
“…exposure are consistent with previously reported global transcriptional profiles (Benton et al., 2006; Fry et al., 2005; Gasch, A. P. et al., 2000; Jelinsky & Samson, 1999) and are reflective of signal amplification through the MEC1 phosphorylation cascade, as effectors HUG1 and RNR3 demonstrated…”
BackgroundResultInfluentialEarly and late responses to timed alkylation damage in alkyladenine DNA glycosylase animal models.
Aljohani, A. S. M. (2017) · Surrey Research Insight Open Access (The University of Surrey)
Mitochondria Remodeling in Cancer
Dornfeld, K. J., & Skildum, A. J. (2018) · Springer eBooks · doi:10.1007/978-3-319-73344-9_9
Accounting for programmed ribosomal frameshifting in the computation of codonPreprint
García, V., Zoller, S., & Anisimova, M. O. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/293340
“Transcriptome data for mRNA levels were obtained from (Holstege et al. 1998; Arava et al. 2003; Holland 2002; Jelinsky and Samson 1999; Roth et al. 1998).”
MethodTranscriptional Responses to DNA Damage
Friedberg, E. C., Walker, G. C., Siede, W., Wood, R. D., Schultz, R. A., & Ellenberger, T. E. (2014) · ASM Press eBooks · doi:10.1128/9781555816704.ch22
Aspen Cancer Conference Fellows
(2004) · Toxicologic Pathology · doi:10.1080/01926230490882358
Pérez-Ortín, J. E., del Olmo, M., & García‐Martínez, J. (2008) · Springer eBooks · doi:10.1007/978-3-540-85463-0_26
Mera, N., Aoyagi, H., Nakasono, S., Iwasaki, K., Saiki, H., & Tanaka, H. (2004) · Journal of Bioscience and Bioengineering · doi:10.1263/jbb.97.169
Cellular and Molecular Responses to Alkylation Damage in DNA
Bugni, J. M., & Samson, L. D. (2005) · CRC Press eBooks · doi:10.1201/9780849352683.pt7
Self-citationLeikauf, G. D., & Ramos, K. S. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-801238-3.01938-3
A Review on Bioinformatics: Computational Approaches to Drug Discovery and Development
Ullah, M. F., Bashir, M., Ain, Q. U., Mohammed, S. H., Gupta, M., Kallel, M., & Batool, N. (2025) · Nano LIFE · doi:10.1142/s1793984425420036
Du, Y., Lin, A., Brown, J. A. R., Howe, L. J., & Xao, W. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.06.723303
“These genes were strongly induced by a DNA-damaging agent methyl methanesulfonate (MMS) (Fu et al., 2008; Gasch et al., 2000; Jelinsky and Samson, 1999).”
Atlas of stress-induced changes in yeast transfer RNA modification levelsPreprint
Radešić, M., Pedor, J. K., Qasim, M. S., Rajaveräjä, A.-E., Sipari, N., & Sarin, L. P. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.17.745200
Du, Y., Lin, A., Brown, J. A., Howe, L. J., & Xiao, W. (2026) · eLife · doi:10.7554/elife.111823
Du, Y., Lin, A., Brown, J. A., Howe, L. J., & Xiao, W. (2026) · eLife · doi:10.7554/elife.111823.1
Nees, M., Kusnezow, W., & Woodworth, C. D. (2006) · Elsevier eBooks · doi:10.1016/b978-012088561-9/50003-x
Sánchez (2002) · doi:10.1379/1466-1268(2002)007
Metadata
- Authors
- Jelinsky, S. A., & Samson, L. D.
- Affiliations
- Harvard University (US)
- Corresponding author
- Samson, Leona D.
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 1999-02-16
- Volume
- 96
- Issue
- 4
- Pages
- 1486-1491
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC15489
- OpenAlex
- W2155675863
- Cited by
- 419
- References
- 36
- Citations by year
- 2026: 4 · 2025: 1 · 2024: 4 · 2023: 4 · 2022: 2 · 2021: 1 · 2020: 5 · 2019: 6 · 2018: 6 · 2017: 4 · 2016: 5 · 2015: 11 · 2014: 10 · 2013: 8 · 2012: 11
- FWCI
- 17.46
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (5p01hg001323-03)
- National Human Genome Research Institute (P01 HG 01323)
- National Cancer Institute (CA-55042, CA09078, T32CA009078, R01CA055042)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- Saccharomyces cerevisiae, methyl methanesulfonate, alkylating agents, DNA damage response, gene expression profiling, transcriptome, DNA repair genes
- MeSH terms
- Alkylating Agents, DNA Damage, Fungal Proteins, Genes, Fungal, Methyl Methanesulfonate, Saccharomyces cerevisiae, Transcription, Genetic, Open Reading Frames, Genome, Fungal
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
